Align ABC transporter for D-Trehalose, permease component 1 (characterized)
to candidate SM_b21459 SM_b21459 sugar uptake ABC transporter permease
Query= reanno::Smeli:SM_b20326 (328 letters) >FitnessBrowser__Smeli:SM_b21459 Length = 297 Score = 309 bits (791), Expect = 6e-89 Identities = 156/304 (51%), Positives = 207/304 (68%), Gaps = 13/304 (4%) Query: 23 LQAQRVRSAWLFLAPTFLVLALVAGWPLIRTIYFSFTNASLTNLSGAEFVGFANYLSWIT 82 ++ Q+ R+AW+FL P L L VA WPL R+I+FSFT+A L S FVG N++ Sbjct: 7 MERQQRRTAWIFLLPLLLTLMAVAIWPLARSIFFSFTDAYLDAPSDYGFVGIENFVE--- 63 Query: 83 LKSGRTIYRGLLADPAWWNAVWNTLKFTVLSVSIETALGLIVALVLNAQFPGRGLVRAAI 142 + DP +W AV NTL FT++SV +ET LGL +AL+L+ F GRG+VRAAI Sbjct: 64 ----------VAEDPVFWGAVRNTLVFTLVSVGLETLLGLAIALLLHRAFLGRGIVRAAI 113 Query: 143 LIPWAIPTIVSAKMWAWMLNDQFGILNDMLIGLGLIGEKIAWTASPDTAMIAELIVDVWK 202 LIPWA+P +VSA++W WMLNDQFG++N +L+ LGL+ + +AWTA P + + +DVW Sbjct: 114 LIPWAMPMVVSARIWEWMLNDQFGLINKLLVALGLVEKGVAWTADPSLILGTVIFIDVWV 173 Query: 203 TTPFMALLILAGLQMVPGDIYEAAKIDGVHPVRVFWRVTLPLIRPALMVAVIFRMLDALR 262 TTPFM LLILAGLQ++P +IYEAA + GV + FW +TLPL PA+ VA++FR LDALR Sbjct: 174 TTPFMVLLILAGLQLIPEEIYEAADVSGVPQWKRFWSITLPLATPAIGVAILFRTLDALR 233 Query: 263 IFDLIYVLTPNNAQTKTMSVMARENLFDFDKFAYGAAASTMLFLIIATITILYMWLGRLN 322 +FDL YVL NN T TMS+ AR+ L F GAAAST +F+II I I+ + L RL+ Sbjct: 234 MFDLSYVLAANNENTMTMSIYARDQLISFQDLGLGAAASTWVFMIIGLIAIVIVGLLRLD 293 Query: 323 LSGG 326 + G Sbjct: 294 RATG 297 Lambda K H 0.328 0.140 0.438 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 376 Number of extensions: 18 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 328 Length of database: 297 Length adjustment: 27 Effective length of query: 301 Effective length of database: 270 Effective search space: 81270 Effective search space used: 81270 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory